Magnesium in PDB 5v8x: Mutant Structures of Streptococcus Agalactiae Gbs Glyceraldehyde-3- Phosphate Dehydrogenase (Gapdh)

The structure of Mutant Structures of Streptococcus Agalactiae Gbs Glyceraldehyde-3- Phosphate Dehydrogenase (Gapdh), PDB code: 5v8x was solved by N.Schormann, G.C.Ulett, D.Chattopadhyay, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	46.80 / 2.95
Space group	P 1 21 1
Cell size a, b, c (Å), α, β, γ (°)	68.104, 107.805, 91.432, 90.00, 105.73, 90.00
R / Rfree (%)	22.2 / 27

The binding sites of Magnesium atom in the Mutant Structures of Streptococcus Agalactiae Gbs Glyceraldehyde-3- Phosphate Dehydrogenase (Gapdh) (pdb code 5v8x). This binding sites where shown within 5.0 Angstroms radius around Magnesium atom.
In total 4 binding sites of Magnesium where determined in the Mutant Structures of Streptococcus Agalactiae Gbs Glyceraldehyde-3- Phosphate Dehydrogenase (Gapdh), PDB code: 5v8x:
Jump to Magnesium binding site number: 1; 2; 3; 4;

Magnesium binding site 1 out of 4 in the Mutant Structures of Streptococcus Agalactiae Gbs Glyceraldehyde-3- Phosphate Dehydrogenase (Gapdh)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 1 of Mutant Structures of Streptococcus Agalactiae Gbs Glyceraldehyde-3- Phosphate Dehydrogenase (Gapdh) within 5.0Å range: probe atom residue distance (Å) B Occ A:Mg402 b:65.3 occ:1.00 O A:ILE21 2.4 65.4 1.0 O A:VAL27 2.6 77.6 1.0 O A:VAL24 3.0 79.0 1.0 C A:ILE21 3.5 65.7 1.0 C A:VAL27 3.8 77.4 1.0 CG2 A:ILE21 3.8 67.6 1.0 O A:GLN22 3.8 75.2 1.0 CA A:GLN22 3.9 67.9 1.0 CA A:GLU28 4.0 84.5 1.0 C A:GLN22 4.0 69.2 1.0 C A:VAL24 4.1 82.1 1.0 N A:GLN22 4.1 67.7 1.0 CB A:GLU28 4.2 86.5 1.0 N A:GLU28 4.4 81.0 1.0 N A:VAL24 4.5 70.5 1.0 CA A:ILE21 4.6 64.5 1.0 CG A:GLU28 4.8 88.4 1.0 CB A:ILE21 4.8 63.5 1.0 CA A:VAL24 4.8 75.4 1.0 N A:ASN23 5.0 70.0 1.0 CA A:VAL27 5.0 76.6 1.0

Magnesium binding site 2 out of 4 in the Mutant Structures of Streptococcus Agalactiae Gbs Glyceraldehyde-3- Phosphate Dehydrogenase (Gapdh)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 2 of Mutant Structures of Streptococcus Agalactiae Gbs Glyceraldehyde-3- Phosphate Dehydrogenase (Gapdh) within 5.0Å range: probe atom residue distance (Å) B Occ B:Mg402 b:65.1 occ:1.00 O B:VAL27 2.4 73.0 1.0 O B:ILE21 2.4 71.0 1.0 O B:VAL24 2.6 82.7 1.0 C B:VAL27 3.5 77.0 1.0 C B:ILE21 3.5 71.0 1.0 C B:VAL24 3.7 88.2 1.0 O B:GLN22 3.8 87.0 1.0 CG2 B:ILE21 3.9 70.0 1.0 CA B:GLU28 3.9 80.8 1.0 CA B:GLN22 4.0 77.3 1.0 C B:GLN22 4.1 80.5 1.0 CB B:GLU28 4.2 85.4 1.0 N B:GLU28 4.2 73.7 1.0 N B:GLN22 4.2 73.6 1.0 N B:VAL24 4.3 82.9 1.0 O B:GLU25 4.6 85.2 1.0 CA B:VAL24 4.6 88.3 1.0 N B:GLU25 4.6 92.1 1.0 CA B:ILE21 4.6 70.8 1.0 CA B:VAL27 4.7 83.6 1.0 CA B:GLU25 4.7 95.7 1.0 N B:VAL27 4.7 85.6 1.0 C B:GLU25 4.8 90.0 1.0 CB B:ILE21 4.9 69.7 1.0 CG B:GLU28 4.9 88.2 1.0 N B:ASN23 5.0 81.0 1.0 CG1 B:VAL27 5.0 89.1 1.0

Magnesium binding site 3 out of 4 in the Mutant Structures of Streptococcus Agalactiae Gbs Glyceraldehyde-3- Phosphate Dehydrogenase (Gapdh)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 3 of Mutant Structures of Streptococcus Agalactiae Gbs Glyceraldehyde-3- Phosphate Dehydrogenase (Gapdh) within 5.0Å range: probe atom residue distance (Å) B Occ C:Mg402 b:99.6 occ:1.00 O C:VAL24 2.4 0.4 1.0 O C:ILE21 2.4 0.8 1.0 O C:VAL27 2.6 98.5 1.0 C C:VAL24 3.4 0.8 1.0 C C:ILE21 3.6 97.2 1.0 O C:GLN22 3.6 0.3 1.0 C C:VAL27 3.8 98.3 1.0 C C:GLN22 3.9 0.1 1.0 CA C:GLN22 4.0 0.2 1.0 N C:VAL24 4.1 0.8 1.0 CG2 C:ILE21 4.2 83.3 1.0 N C:GLU25 4.2 0.1 1.0 CA C:GLU25 4.2 0.4 1.0 N C:GLN22 4.2 97.7 1.0 CA C:GLU28 4.3 0.4 1.0 CA C:VAL24 4.3 0.7 1.0 N C:GLU28 4.5 99.3 1.0 CB C:GLU28 4.5 0.5 1.0 CA C:ILE21 4.7 90.2 1.0 N C:VAL27 4.7 0.1 1.0 N C:ASN23 4.8 0.9 1.0 CG1 C:VAL27 4.8 97.5 1.0 C C:GLU25 4.9 0.2 1.0 CA C:VAL27 4.9 99.5 1.0 CB C:VAL24 4.9 0.0 1.0 N C:GLY26 5.0 0.9 1.0

Magnesium binding site 4 out of 4 in the Mutant Structures of Streptococcus Agalactiae Gbs Glyceraldehyde-3- Phosphate Dehydrogenase (Gapdh)


Mono view


Stereo pair view

A full contact list of Magnesium with other atoms in the Mg binding site number 4 of Mutant Structures of Streptococcus Agalactiae Gbs Glyceraldehyde-3- Phosphate Dehydrogenase (Gapdh) within 5.0Å range: probe atom residue distance (Å) B Occ D:Mg402 b:80.9 occ:1.00 O D:VAL24 2.3 97.8 1.0 O D:VAL27 2.5 99.0 1.0 O D:ILE21 2.6 0.3 1.0 C D:VAL24 3.5 0.7 1.0 C D:ILE21 3.7 97.0 1.0 C D:VAL27 3.8 0.4 1.0 O D:GLN22 3.9 0.6 1.0 CG1 D:VAL24 4.0 0.9 1.0 N D:VAL24 4.2 0.6 1.0 C D:GLN22 4.2 99.4 1.0 CA D:GLN22 4.2 97.4 1.0 CG2 D:ILE21 4.3 0.5 1.0 CA D:GLU28 4.3 0.1 1.0 CA D:VAL24 4.4 0.9 1.0 CB D:GLU28 4.4 0.5 1.0 N D:GLN22 4.5 95.1 1.0 N D:GLU25 4.5 0.8 1.0 N D:GLU28 4.5 0.7 1.0 CA D:GLU25 4.6 0.9 1.0 CG1 D:VAL27 4.7 0.9 1.0 CG D:GLU28 4.7 1.0 1.0 CB D:VAL24 4.8 0.4 1.0 N D:VAL27 4.8 0.5 1.0 CA D:ILE21 4.9 96.9 1.0 OE1 D:GLU28 4.9 0.6 1.0 CA D:VAL27 4.9 0.3 1.0

N.Schormann, G.C.Ulett, D.Chattopadhyay. Mutant Structures of Streptococcus Agalactiae Gbs Glyceraldehyde-3-Phosphate Dehydrogenase (Gapdh) To Be Published.